Seems unable to find input faa files

[ganiatgithub]

Hello,

Hope it's not a very obvious mistake from my side. I used the following command:

phylophlan \
--input_folder /home/gnii0001/rp24/gaofeng/projects/02_acidic_nitritation/data/faa \
--output_folder /home/gnii0001/rp24/gaofeng/projects/02_acidic_nitritation/result/phylophlan \
--nproc 24 \
--diversity medium \
-t a \
-d phylophlan \
-f /home/gnii0001/rp24/gaofeng/tools/Miniconda3/envs/phylophlan/bin/configs/supermatrix_aa.cfg \
--proteome_extension "faa.gz" \
-i wgt 2>&1 | tee phylophlan.log

Here is my error:

Loading files from "/home/gnii0001/rp24/gaofeng/projects/02_acidic_nitritation/data/faa"
Loading files from "/home/gnii0001/rp24/gaofeng/projects/02_acidic_nitritation/data/faa"
Inputs already checked
[e] no inputs found, please check your params and inputs file extensions

However, the input folder contains the zipped faa files:

ls /home/gnii0001/rp24/gaofeng/projects/02_acidic_nitritation/data/faa
sewage_bin1.faa.gz   sewage_bin2.faa.gz   sewage_bin3.faa.gz   sewage_bin4.faa.gz   sewage_bin6.faa.gz  urine_bin16.faa.gz
sewage_bin10.faa.gz  sewage_bin20.faa.gz  sewage_bin30.faa.gz  sewage_bin40.faa.gz  sewage_bin7.faa.gz  urine_bin17.faa.gz
sewage_bin11.faa.gz  sewage_bin21.faa.gz  sewage_bin31.faa.gz  sewage_bin41.faa.gz  sewage_bin8.faa.gz  urine_bin18.faa.gz
sewage_bin12.faa.gz  sewage_bin22.faa.gz  sewage_bin32.faa.gz  sewage_bin42.faa.gz  sewage_bin9.faa.gz  urine_bin2.faa.gz
sewage_bin13.faa.gz  sewage_bin23.faa.gz  sewage_bin33.faa.gz  sewage_bin43.faa.gz  urine_bin1.faa.gz   urine_bin3.faa.gz
sewage_bin14.faa.gz  sewage_bin24.faa.gz  sewage_bin34.faa.gz  sewage_bin44.faa.gz  urine_bin10.faa.gz  urine_bin4.faa.gz
sewage_bin15.faa.gz  sewage_bin25.faa.gz  sewage_bin35.faa.gz  sewage_bin45.faa.gz  urine_bin11.faa.gz  urine_bin5.faa.gz
sewage_bin16.faa.gz  sewage_bin26.faa.gz  sewage_bin36.faa.gz  sewage_bin46.faa.gz  urine_bin12.faa.gz  urine_bin6.faa.gz
sewage_bin17.faa.gz  sewage_bin27.faa.gz  sewage_bin37.faa.gz  sewage_bin47.faa.gz  urine_bin13.faa.gz  urine_bin7.faa.gz
sewage_bin18.faa.gz  sewage_bin28.faa.gz  sewage_bin38.faa.gz  sewage_bin48.faa.gz  urine_bin14.faa.gz  urine_bin8.faa.gz
sewage_bin19.faa.gz  sewage_bin29.faa.gz  sewage_bin39.faa.gz  sewage_bin5.faa.gz   urine_bin15.faa.gz  urine_bin9.faa.gz

The log file is the same as the error here. I've tried not specifying extension, not using quotation marks, or using unzipped faa files, not working and I cannot think of any good reason. Any tips?

Kind regards

[fasnicar]

Hi, first of all, thanks for using PhyloPhlAn!

So, I think the problem is with the --proteome_extension "faa.gz", you don't actually need to provide the compressed extension there. What should actually be specified is an extension to discriminate between genomes and proteomes. Considering all your inputs are .faa.gz and .faa is the default extension for proteomes in PhyloPhlAn, you should be fine by just removing that parameter.

I would suggest also removing the output folder and then re-running the command, additionally what you can specify is the --verbose param that might help de-bug future issues.

Many thanks, Francesco